BN0737 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 4.0699e-05 4.4385e-04
Layer 5 1.6409e-04 8.8438e-04
Layer 3 1.6855e-04 3.0025e-02
Layer 6 4.2540e-04 3.9010e-03
Layer 2 2.5528e-03 9.2158e-02
WM 2.2236e-02 1.5289e-01
Layer 1 6.8167e-01 5.5479e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 3.0312 0.7572
RTN1 Layer 5 2.5508 0.6852
TUBB2A Layer 5 3.0586 0.6852
HINT1 Layer 5 2.7969 0.6827
SERPINI1 Layer 4 2.9336 0.6701
MORF4L1 Layer 4 2.6250 0.6689
NDRG4 Layer 5 3.0586 0.6683
STMN2 Layer 5 3.2227 0.6669
CPLX1 Layer 5 2.7715 0.6651
ATP5F1B Layer 4 2.5117 0.6632
UCHL1 Layer 4 2.3105 0.6600
NELL2 Layer 5 2.8711 0.6592
SOD1 Layer 4 2.5605 0.6588
STXBP1 Layer 4 3.0449 0.6583
SH3GL2 Layer 5 2.7246 0.6579
SYP Layer 5 3.0859 0.6574
SYN2 Layer 5 2.9023 0.6570
TAGLN3 Layer 5 2.7539 0.6526
STMN1 Layer 5 2.6426 0.6491
ATP1A1 Layer 5 2.7598 0.6486
NSF Layer 5 2.5449 0.6471
ANXA6 Layer 5 2.9336 0.6467
YWHAH Layer 4 2.5059 0.6456
DCLK1 Layer 4 2.7363 0.6450
BASP1 Layer 5 2.4883 0.6441
SARAF Layer 5 2.3594 0.6423
OAT Layer 5 2.3438 0.6423
ACTG1 Layer 5 2.3340 0.6419
APP Layer 5 2.5273 0.6402
DYNC1H1 Layer 5 2.3242 0.6402
COX6C Layer 5 2.3125 0.6380
NAPB Layer 5 2.9023 0.6377
TPI1 Layer 5 2.7012 0.6375
DNAJC6 Layer 5 2.7422 0.6370
CHGA Layer 4 2.8145 0.6368
ATP6V1B2 Layer 5 2.7715 0.6368
BSCL2 Layer 5 2.7422 0.6359
MDH1 Layer 5 2.7422 0.6351
SLC24A2 Layer 4 2.3711 0.6349
NGRN Layer 4 2.6777 0.6343
RAB6B Layer 5 2.6602 0.6341
RTN3 Layer 6 2.2930 0.6341
TRIM2 Layer 5 2.4336 0.6341
RAB3A Layer 4 2.6777 0.6337
PJA2 Layer 5 2.7305 0.6335
SYT1 Layer 5 2.5176 0.6327
G3BP2 Layer 4 2.7480 0.6325
RGS4 Layer 5 2.8965 0.6317
ENO2 Layer 5 2.7363 0.6313
NEFL Layer 5 2.5215 0.6311

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0737
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0737_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0737/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0737/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0737/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0737/report/PD/BN0737_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0737/report/PD/BN0737_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 01:28:58
  • Number of Processes: 10
  • Spending Time: 0h 3m